9-87453594-T-C

Variant names:

• chr9-87453594-T-C
• rs10124291

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.672 in 152,190 control chromosomes in the GnomAD database, including 34,590 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.67 (34590 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.731
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102128 AN: 152072 Hom.: 34541 Cov.: 34

Gnomad AFR AF: 0.610

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.766

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.683

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.672 AC: 102228 AN: 152190 Hom.: 34590 Cov.: 34 AF XY: 0.674 AC XY: 50111 AN XY: 74402

African (AFR) AF: 0.610 AC: 25317 AN: 41502

American (AMR) AF: 0.736 AC: 11258 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.766 AC: 2659 AN: 3470

East Asian (EAS) AF: 0.809 AC: 4198 AN: 5186

South Asian (SAS) AF: 0.817 AC: 3941 AN: 4822

European-Finnish (FIN) AF: 0.652 AC: 6903 AN: 10584

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45733 AN: 68010

Other (OTH) AF: 0.685 AC: 1447 AN: 2112

Alfa AF: 0.678 Hom.: 147194

Bravo AF: 0.675

Asia WGS AF: 0.820 AC: 2853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		-0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10124291; hg19: chr9-90068509;